dmriprep.utils package¶

Submodules¶

exception dmriprep.utils.bids.BIDSError(message, bids_root)[source]¶: Bases: ValueError

exception dmriprep.utils.bids.BIDSWarning[source]¶: Bases: RuntimeWarning

dmriprep.utils.bids.collect_data(bids_dir, participant_label, concat_dwis, session_label=None)[source]¶: Uses pybids to retrieve the input data for a given participant

dmriprep.utils.bids.collect_participants(bids_dir, participant_label=None, strict=False, bids_validate=True)[source]¶: List the participants under the BIDS root and checks that participants designated with the participant_label argument exist in that folder. Returns the list of participants to be finally processed. Requesting all subjects in a BIDS directory root: >>> collect_participants(str(datadir / ‘ds114’), bids_validate=False) [‘01’, ‘02’, ‘03’, ‘04’, ‘05’, ‘06’, ‘07’, ‘08’, ‘09’, ‘10’] Requesting two subjects, given their IDs: >>> collect_participants(str(datadir / ‘ds114’), participant_label=[‘02’, ‘04’], … bids_validate=False) [‘02’, ‘04’] Requesting two subjects, given their IDs (works with ‘sub-‘ prefixes): >>> collect_participants(str(datadir / ‘ds114’), participant_label=[‘sub-02’, ‘sub-04’], … bids_validate=False) [‘02’, ‘04’] Requesting two subjects, but one does not exist: >>> collect_participants(str(datadir / ‘ds114’), participant_label=[‘02’, ‘14’], … bids_validate=False) [‘02’] >>> collect_participants( … str(datadir / ‘ds114’), participant_label=[‘02’, ‘14’], … strict=True, bids_validate=False) # doctest: +IGNORE_EXCEPTION_DETAIL Traceback (most recent call last): dmriprep.utils.bids.BIDSError: …

dmriprep.utils.bids.group_dwi(dwi_files, session_list=None, concat_dwis=None)[source]¶

dmriprep.utils.bids.validate_input_dir(bids_dir, subject_list)[source]¶

dmriprep.utils.hemisphere.is_hemispherical(vecs)[source]¶

Test whether all points on a unit sphere lie in the same hemisphere.

Inputs

vecsnumpy.ndarray: 2D numpy array with shape (N, 3) where N is the number of points. All points must lie on the unit sphere.

Outputs

is_hemibool: If True, one can find a hemisphere that contains all the points. If False, then the points do not lie in any hemisphere
polenumpy.ndarray: If is_hemi == True, then pole is the “central” pole of the input vectors. Otherwise, pole is the zero vector.

References